Reduced-bias gamma diversity of a metacommunity

Calculates the reduced-bias diversity of order \(q\) of a metacommunity.

Usage

GammaDiversity(MC, q = 1, Correction = "Best", Tree = NULL, Normalize = TRUE, 
  Z = NULL, CheckArguments = TRUE)

Arguments

MC: A MetaCommunity object.
q: A number: the order of diversity. Default is 1.
Correction: A string containing one of the possible corrections accepted by AlphaEntropy or "None" or "Best", the default value.
Tree: An object of class hclust, "phylo" (see read.tree), phylog or PPtree. The tree must be ultrametric.
Normalize: If TRUE (default), diversity is not affected by the height of the tree.
If FALSE, diversity is proportional to the height of the tree.
Z: A relatedness matrix, i.e. a square matrix whose terms are all positive, strictly positive on the diagonal. Generally, the matrix is a similarity matrix, i.e. the diagonal terms equal 1 and other terms are between 0 and 1.
CheckArguments: Logical; if TRUE, the function arguments are verified. Should be set to FALSE to save time when the arguments have been checked elsewhere.

Details

Entropy is calculated by GammaEntropy and transformed into diversity.

Value

The metacommunity's gamma entropy.

References

Marcon, E., Scotti, I., Herault, B., Rossi, V. and Lang, G. (2014). Generalization of the partitioning of Shannon diversity. PLOS One 9(3): e90289.

Marcon, E., Herault, B. (2015). Decomposing Phylodiversity. Methods in Ecology and Evolution 6(3): 333-339.

Marcon, E., Zhang, Z. and Herault, B. (2014). The decomposition of similarity-based diversity and its bias correction. HAL hal-00989454(version 3).

Examples

# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest)
data(Paracou618)
# Calculate Simpson gamma diversity
GammaDiversity(Paracou618.MC, 2)
#>  UnveilJ 
#> 73.09335 
# Compare without correction
GammaDiversity(Paracou618.MC, 2, Correction = "None")
#>    None 
#> 68.7215 
# Estimate phylogenetic Simpson gamma diversity
GammaDiversity(Paracou618.MC, 2, Tree = Paracou618.Taxonomy)   
#> [1] 25.11451